#!/usr/bin/perl
#Programmer: Rory Carmichael
#Purpose: write a makefile to align everything

my $groupdir = shift;

foreach my $file (`ls $groupdir`) {
	chomp $file;
	print "$file.fasta: $groupdir/$file muscle\n";
	print "\tmuscle -in $groupdir/$file -out $file.fasta\n\n";
}
